Research workbench
Structure of VPS4B in complex with an allele-specific covalent inhibitor
Analyse Structure of VPS4B in complex with an allele-specific covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L9X
- Type
- protein
- Length
- 300 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 4B
- EC
- 3.6.4.6
- UniProt
- O75351
- Ligands
- XQV, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 4B (EC 3.6.4.6) | protein | 300 | 43% helix, 15% strand | O75351 |
Ligands and binding sites
- XQV · N-{3-[(8-phenyl[1,2,4]triazolo[1,5-a]pyridin-2-yl) amino]phenyl}propanamide · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.69 | 0.82 | 47 | empty |
| 2 | 136 | 0.48 | 0.78 | 29 | XQV, SO4 |
| 3 | 61 | 0.40 | 0.80 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7L9X · Structure of VPS4B in complex with an allele-specific covalent inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- O75351 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 4B… · a predicted model of the same protein · chain A against A, TM-score 0.93
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O75351
- Elsewhere: RCSB PDB 7L9X · PDBe 7L9X · UniProt O75351
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